[2023-03-18 00:13:25,308] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:13:25,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:13:25,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference
[2023-03-18 00:13:26,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:13:26,443] [INFO] Task started: Prodigal
[2023-03-18 00:13:26,443] [INFO] Running command: cat /var/lib/cwl/stg4bb4284c-27b3-4bb5-9db8-992f49ee8bfa/OceanDNA-b13448.fa | prodigal -d OceanDNA-b13448/cds.fna -a OceanDNA-b13448/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:13:37,023] [INFO] Task succeeded: Prodigal
[2023-03-18 00:13:37,024] [INFO] Task started: HMMsearch
[2023-03-18 00:13:37,024] [INFO] Running command: hmmsearch --tblout OceanDNA-b13448/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/reference_markers.hmm OceanDNA-b13448/protein.faa > /dev/null
[2023-03-18 00:13:37,190] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:13:37,191] [INFO] Found 6/6 markers.
[2023-03-18 00:13:37,207] [INFO] Query marker FASTA was written to OceanDNA-b13448/markers.fasta
[2023-03-18 00:13:37,209] [INFO] Task started: Blastn
[2023-03-18 00:13:37,209] [INFO] Running command: blastn -query OceanDNA-b13448/markers.fasta -db /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/reference_markers.fasta -out OceanDNA-b13448/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:13:37,786] [INFO] Task succeeded: Blastn
[2023-03-18 00:13:37,787] [INFO] Selected 16 target genomes.
[2023-03-18 00:13:37,787] [INFO] Target genome list was writen to OceanDNA-b13448/target_genomes.txt
[2023-03-18 00:13:37,798] [INFO] Task started: fastANI
[2023-03-18 00:13:37,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb4284c-27b3-4bb5-9db8-992f49ee8bfa/OceanDNA-b13448.fa --refList OceanDNA-b13448/target_genomes.txt --output OceanDNA-b13448/fastani_result.tsv --threads 1
[2023-03-18 00:13:45,238] [INFO] Task succeeded: fastANI
[2023-03-18 00:13:45,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:13:45,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:13:45,256] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:13:45,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:13:45,256] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	80.5929	400	723	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	80.4913	403	723	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.6311	347	723	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	79.6195	347	723	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	79.5862	321	723	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	79.3642	329	723	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	79.3562	337	723	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.3174	350	723	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	79.2803	339	723	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.2071	334	723	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	79.1964	359	723	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	79.1292	343	723	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	78.7404	265	723	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	78.2517	302	723	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	78.1811	249	723	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	77.6191	199	723	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:13:45,256] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13448/tc_result.tsv
[2023-03-18 00:13:45,257] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:13:45,257] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:13:45,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/checkm_data
[2023-03-18 00:13:45,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:13:45,365] [INFO] Task started: CheckM
[2023-03-18 00:13:45,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13448/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13448/checkm_input OceanDNA-b13448/checkm_result
[2023-03-18 00:14:15,659] [INFO] Task succeeded: CheckM
[2023-03-18 00:14:15,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.87%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:14:15,666] [INFO] ===== Completeness check finished =====
[2023-03-18 00:14:15,667] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:14:15,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13448/markers.fasta)
[2023-03-18 00:14:15,668] [INFO] Task started: Blastn
[2023-03-18 00:14:15,668] [INFO] Running command: blastn -query OceanDNA-b13448/markers.fasta -db /var/lib/cwl/stg83e695cc-c89d-465c-bc95-c8bcf0eb46ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13448/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:14:16,515] [INFO] Task succeeded: Blastn
[2023-03-18 00:14:16,516] [INFO] Selected 8 target genomes.
[2023-03-18 00:14:16,516] [INFO] Target genome list was writen to OceanDNA-b13448/target_genomes_gtdb.txt
[2023-03-18 00:14:16,528] [INFO] Task started: fastANI
[2023-03-18 00:14:16,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb4284c-27b3-4bb5-9db8-992f49ee8bfa/OceanDNA-b13448.fa --refList OceanDNA-b13448/target_genomes_gtdb.txt --output OceanDNA-b13448/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:14:21,247] [INFO] Task succeeded: fastANI
[2023-03-18 00:14:21,253] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:14:21,253] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002685075.1	s__Poseidonibacter sp002685075	99.6325	624	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	88.9605	559	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	87.2982	517	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCA_905479135.1	s__Poseidonibacter sp905479135	84.5716	310	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	84.4791	500	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	83.0776	450	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	80.5685	402	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.5523	331	723	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:14:21,254] [INFO] GTDB search result was written to OceanDNA-b13448/result_gtdb.tsv
[2023-03-18 00:14:21,254] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:14:21,256] [INFO] DFAST_QC result json was written to OceanDNA-b13448/dqc_result.json
[2023-03-18 00:14:21,257] [INFO] DFAST_QC completed!
[2023-03-18 00:14:21,257] [INFO] Total running time: 0h0m56s